4XII

X-ray structure of human butyrylcholinesterase in complex with N-((1-(2,3-dihydro-1H-inden-2-yl)piperidin-3-yl)methyl)-8-hydroxy-N-(2-methoxyethyl)-5-nitroquinoline-7-carboxamide

PDB DOI: https://doi.org/10.2210/pdb4XII/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Insect cell expression vector pTIE1
Mutation(s): No

Deposited: 2015-01-07 Released: 2015-07-08
Deposition Author(s): Knez, D., Boris, B., Coquelle, N., Sosic, I., Sink, R., Brazzolotto, X., Mravljak, J., Colletier, J.P., Gobec, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.257
R-Value Work: 0.206
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 129.52 kDa
Atom Count: 8,849
Modelled Residue Count: 1,053
Deposited Residue Count: 1,088
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinesterase	A, B	544	Homo sapiens	Mutation(s): 0 Gene Names: BCHE, CHE1 EC: 3.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P06276 (Homo sapiens) Explore P06276 Go to UniProtKB: P06276
PHAROS: P06276 GTEx: ENSG00000114200
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06276
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G28454KX GlyCosmos: G28454KX GlyGen: G28454KX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F, G	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Focus chain G Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
40V Query on 40V Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain S [auth B] MOL2 format, chain H [auth A] MOL2 format, chain S [auth B]	H [auth A], S [auth B]	N-{[(3R)-1-(2,3-dihydro-1H-inden-2-yl)piperidin-3-yl]methyl}-8-hydroxy-N-(2-methoxyethyl)-5-nitroquinoline-7-carboxamide C₂₈ H₃₂ N₄ O₅ XTNPQSRETUCLAG-LJQANCHMSA-N		Interactions Focus chain H [auth A] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain S [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] I [auth A] K [auth A] T [auth B] AA [auth B], BA [auth B], I [auth A], K [auth A], T [auth B], U [auth B], V [auth B], W [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain I [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain I [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
FUL Query on FUL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain X [auth B] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain X [auth B]	J [auth A], M [auth A], X [auth B]	beta-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-KGJVWPDLSA-N		Interactions Focus chain J [auth A] Focus chain M [auth A] Focus chain X [auth B] Interactions & Density Focus chain J [auth A] Focus chain M [auth A] Focus chain X [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A]	DA [auth B], EA [auth B], Q [auth A], R [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain Q [auth A] Focus chain R [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A]	CA [auth B], N [auth A], O [auth A], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain CA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
40V	BindingDB: 4XII	IC50: 215 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.257
R-Value Work: 0.206
R-Value Observed: 0.208
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.04	α = 90
b = 79.76	β = 90
c = 230.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-07-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-08
Type: Initial release
Version 1.1: 2015-07-22
Changes: Database references
Version 1.2: 2015-08-05
Changes: Database references
Version 1.3: 2019-10-09
Changes: Data collection, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary